In-cell structure analysis of antisense Gadd45α SINEB2-a deletion mutants

SINEUPs are SINE repeat element containig long non-coding RNAs (lncRNAs)which positively regulate target mRNA translation at post-transcription level. SINE RNA region is crucial for SINEUP function. To analyze the effect of sequence deletion on RNA secondary structure of SINEB2 RNA derived from mouse natural antisense lncRNA to Gadd45α gene, RNA structure of four deletion mutants were chemically probed inside cells. For this, different structure mutants and target EGFP mRNA plasmids were co-transfected in HEK293 cells and icSHAPE libraries were prepared. Two biological replicates of each NAI-N3 and DMSO (mock) treated samples